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Commit 5c4a033f authored by Peter Eastman's avatar Peter Eastman
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Incorporating Cuda code into OpenMM

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Showing with 890 additions and 235 deletions
olla/include/Stream.h
View file @ 5c4a033f
......@@ -107,7 +107,7 @@ public:
* the values should be packed into a single array: all the values for the first element, followed by all the values
* for the next element, etc.
*/
void saveToArray(void* array);
void saveToArray(void* array) const;
/**
* Set every element of this stream to the same value.
*
......
olla/src/Stream.cpp
View file @ 5c4a033f
......@@ -75,7 +75,7 @@ void Stream::loadFromArray(const void* array) {
impl->loadFromArray(array);
}
void Stream::saveToArray(void* array) {
void Stream::saveToArray(void* array) const {
impl->saveToArray(array);
}
......
openmmapi/src/OpenMMContextImpl.cpp
View file @ 5c4a033f
......@@ -66,11 +66,6 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
else if (!platform->supportsKernels(kernelNames))
throw OpenMMException("Specified a Platform for an OpenMMContext which does not support all required kernels");
platform->contextCreated(*this);
positions = platform->createStream("atomPositions", system.getNumAtoms(), Stream::Double3, *this);
velocities = platform->createStream("atomVelocities", system.getNumAtoms(), Stream::Double3, *this);
forces = platform->createStream("atomForces", system.getNumAtoms(), Stream::Double3, *this);
double zero[] = {0.0, 0.0, 0.0};
velocities.fillWithValue(&zero);
kineticEnergyKernel = platform->createKernel(CalcKineticEnergyKernel::Name(), *this);
vector<double> masses(system.getNumAtoms());
for (size_t i = 0; i < masses.size(); ++i)
......@@ -79,6 +74,11 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
for (size_t i = 0; i < forceImpls.size(); ++i)
forceImpls[i]->initialize(*this);
integrator.initialize(*this);
positions = platform->createStream("atomPositions", system.getNumAtoms(), Stream::Double3, *this);
velocities = platform->createStream("atomVelocities", system.getNumAtoms(), Stream::Double3, *this);
forces = platform->createStream("atomForces", system.getNumAtoms(), Stream::Double3, *this);
double zero[] = {0.0, 0.0, 0.0};
velocities.fillWithValue(&zero);
}
OpenMMContextImpl::~OpenMMContextImpl() {
......
platforms/cuda/src/CudaKernelFactory.cpp
View file @ 5c4a033f
......@@ -38,19 +38,19 @@ using namespace OpenMM;
KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform& platform, OpenMMContextImpl& context) const {
_gpuContext* gpu = static_cast<_gpuContext*>(context.getPlatformData());
if (name == CalcStandardMMForceFieldKernel::Name())
return new CudaCalcStandardMMForceFieldKernel(name, platform, gpu);
return new CudaCalcStandardMMForceFieldKernel(name, platform, gpu, context.getSystem());
// if (name == CalcGBSAOBCForceFieldKernel::Name())
// return new CudaCalcGBSAOBCForceFieldKernel(name, platform);
// if (name == IntegrateVerletStepKernel::Name())
// return new CudaIntegrateVerletStepKernel(name, platform);
// if (name == IntegrateLangevinStepKernel::Name())
// return new CudaIntegrateLangevinStepKernel(name, platform);
if (name == IntegrateLangevinStepKernel::Name())
return new CudaIntegrateLangevinStepKernel(name, platform, gpu);
// if (name == IntegrateBrownianStepKernel::Name())
// return new CudaIntegrateBrownianStepKernel(name, platform);
// if (name == ApplyAndersenThermostatKernel::Name())
// return new CudaApplyAndersenThermostatKernel(name, platform);
// if (name == CalcKineticEnergyKernel::Name())
// return new CudaCalcKineticEnergyKernel(name, platform);
if (name == CalcKineticEnergyKernel::Name())
return new CudaCalcKineticEnergyKernel(name, platform);
// if (name == RemoveCMMotionKernel::Name())
// return new CudaRemoveCMMotionKernel(name, platform);
}
platforms/cuda/src/CudaKernels.cpp
View file @ 5c4a033f
This diff is collapsed.
platforms/cuda/src/CudaKernels.h
View file @ 5c4a033f
......@@ -34,6 +34,7 @@
#include "kernels.h"
#include "kernels/gpuTypes.h"
#include "System.h"
class CudaAndersenThermostat;
class CudaBrownianDynamics;
......@@ -48,7 +49,7 @@ namespace OpenMM {
*/
class CudaCalcStandardMMForceFieldKernel : public CalcStandardMMForceFieldKernel {
public:
CudaCalcStandardMMForceFieldKernel(std::string name, const Platform& platform, _gpuContext* gpu) : CalcStandardMMForceFieldKernel(name, platform), gpu(gpu) {
CudaCalcStandardMMForceFieldKernel(std::string name, const Platform& platform, _gpuContext* gpu, System& system) : CalcStandardMMForceFieldKernel(name, platform), gpu(gpu), system(system) {
}
~CudaCalcStandardMMForceFieldKernel();
/**
......@@ -96,8 +97,7 @@ public:
private:
_gpuContext* gpu;
int numAtoms, numBonds, numAngles, numPeriodicTorsions, numRBTorsions, num14;
// int **bondIndexArray, **angleIndexArray, **periodicTorsionIndexArray, **rbTorsionIndexArray, **exclusionArray, **bonded14IndexArray;
// RealOpenMM **bondParamArray, **angleParamArray, **periodicTorsionParamArray, **rbTorsionParamArray, **atomParamArray, **bonded14ParamArray;
System& system;
};
///**
......@@ -172,45 +172,39 @@ private:
// int numConstraints;
// double prevStepSize;
//};
//
///**
// * This kernel is invoked by LangevinIntegrator to take one time step.
// */
//class CudaIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
//public:
// CudaIntegrateLangevinStepKernel(std::string name, const Platform& platform) : IntegrateLangevinStepKernel(name, platform),
// dynamics(0), shake(0), masses(0), shakeParameters(0), constraintIndices(0) {
// }
// ~CudaIntegrateLangevinStepKernel();
// /**
// * Initialize the kernel, setting up all parameters related to integrator.
// *
// * @param masses the mass of each atom
// * @param constraintIndices each element contains the indices of two atoms whose distance should be constrained
// * @param constraintLengths the required distance between each pair of constrained atoms
// */
// void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
// const std::vector<double>& constraintLengths);
// /**
// * Execute the kernel.
// *
// * @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
// * @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
// * @param forces a Stream of type Double3 containing the force (x, y, z) on each atom
// * @param temperature the temperature of the heat bath
// * @param friction the friction coefficient coupling the system to the heat bath
// * @param stepSize the integration step size
// */
// void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
//private:
// CudaStochasticDynamics* dynamics;
// CudaShakeAlgorithm* shake;
// RealOpenMM* masses;
// RealOpenMM** shakeParameters;
// int** constraintIndices;
// int numConstraints;
// double prevTemp, prevFriction, prevStepSize;
//};
/**
* This kernel is invoked by LangevinIntegrator to take one time step.
*/
class CudaIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
public:
CudaIntegrateLangevinStepKernel(std::string name, const Platform& platform, _gpuContext* gpu) : IntegrateLangevinStepKernel(name, platform), gpu(gpu) {
}
~CudaIntegrateLangevinStepKernel();
/**
* Initialize the kernel, setting up all parameters related to integrator.
*
* @param masses the mass of each atom
* @param constraintIndices each element contains the indices of two atoms whose distance should be constrained
* @param constraintLengths the required distance between each pair of constrained atoms
*/
void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths);
/**
* Execute the kernel.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @param forces a Stream of type Double3 containing the force (x, y, z) on each atom
* @param temperature the temperature of the heat bath
* @param friction the friction coefficient coupling the system to the heat bath
* @param stepSize the integration step size
*/
void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
private:
_gpuContext* gpu;
double prevTemp, prevFriction, prevStepSize;
};
//
///**
// * This kernel is invoked by BrownianIntegrator to take one time step.
......@@ -278,30 +272,30 @@ private:
// CudaAndersenThermostat* thermostat;
// RealOpenMM* masses;
//};
//
///**
// * This kernel is invoked to calculate the kinetic energy of the system.
// */
//class CudaCalcKineticEnergyKernel : public CalcKineticEnergyKernel {
//public:
// CudaCalcKineticEnergyKernel(std::string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) {
// }
// /**
// * Initialize the kernel, setting up the atomic masses.
// *
// * @param masses the mass of each atom
// */
// void initialize(const std::vector<double>& masses);
// /**
// * Execute the kernel.
// *
// * @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
// * @return the kinetic energy of the system
// */
// double execute(const Stream& velocities);
//private:
// std::vector<double> masses;
//};
/**
* This kernel is invoked to calculate the kinetic energy of the system.
*/
class CudaCalcKineticEnergyKernel : public CalcKineticEnergyKernel {
public:
CudaCalcKineticEnergyKernel(std::string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) {
}
/**
* Initialize the kernel, setting up the atomic masses.
*
* @param masses the mass of each atom
*/
void initialize(const std::vector<double>& masses);
/**
* Execute the kernel.
*
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @return the kinetic energy of the system
*/
double execute(const Stream& velocities);
private:
std::vector<double> masses;
};
//
///**
// * This kernel is invoked to remove center of mass motion from the system.
......
platforms/cuda/src/CudaPlatform.cpp
View file @ 5c4a033f
......@@ -43,10 +43,10 @@ CudaPlatform::CudaPlatform() {
registerKernelFactory(CalcStandardMMForceFieldKernel::Name(), factory);
// registerKernelFactory(CalcGBSAOBCForceFieldKernel::Name(), factory);
// registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
// registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
// registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
// registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);
// registerKernelFactory(CalcKineticEnergyKernel::Name(), factory);
registerKernelFactory(CalcKineticEnergyKernel::Name(), factory);
// registerKernelFactory(RemoveCMMotionKernel::Name(), factory);
}
......
platforms/cuda/src/CudaStreamImpl.h
View file @ 5c4a033f
......@@ -157,6 +157,7 @@ void CudaStreamImpl<T>::loadFromArray(const void* array) {
template <class T>
void CudaStreamImpl<T>::saveToArray(void* array) {
stream->Download();
float* data = reinterpret_cast<float*>(stream->_pSysData);
if (baseType == Stream::Float) {
float* arrayData = (float*) array;
......@@ -176,7 +177,6 @@ void CudaStreamImpl<T>::saveToArray(void* array) {
for (int j = 0; j < width; ++j)
arrayData[i*width+j] = (int) data[i*rowOffset+j];
}
stream->Download();
}
template <class T>
......
platforms/cuda/tests/TestCudaLangevinIntegrator.cpp 0 → 100644
View file @ 5c4a033f
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of LangevinIntegrator.
*/
#include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h"
#include "CudaPlatform.h"
#include "StandardMMForceField.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testSingleBond() {
CudaPlatform platform;
System system(2, 0);
system.setAtomMass(0, 2.0);
system.setAtomMass(1, 2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(2, 1, 0, 0, 0);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply a damped harmonic oscillator, so compare it to the analytical solution.
double freq = std::sqrt(1-0.05*0.05);
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::exp(-0.05*time)*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
double expectedSpeed = -0.5*std::exp(-0.05*time)*(0.05*std::cos(freq*time)+freq*std::sin(freq*time));
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
integrator.step(1);
}
// Not set the friction to a tiny value and see if it conserves energy.
integrator.setFriction(5e-5);
context.setPositions(positions);
State state = context.getState(State::Energy);
double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 1000; ++i) {
state = context.getState(State::Energy);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1);
}
}
void testTemperature() {
const int numAtoms = 8;
const double temp = 100.0;
CudaPlatform platform;
System system(numAtoms, 0);
LangevinIntegrator integrator(temp, 2.0, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 2.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numAtoms);
for (int i = 0; i < numAtoms; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(1);
}
ke /= 1000;
double expected = 0.5*numAtoms*3*BOLTZ*temp;
ASSERT_EQUAL_TOL(expected, ke, 3*expected/std::sqrt(1000.0));
}
void testConstraints() {
const int numAtoms = 8;
const int numConstraints = numAtoms-1;
const double temp = 100.0;
CudaPlatform platform;
System system(numAtoms, numConstraints);
LangevinIntegrator integrator(temp, 2.0, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 10.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numConstraints; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numAtoms);
vector<Vec3> velocities(numAtoms);
init_gen_rand(0);
for (int i = 0; i < numAtoms; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions);
for (int j = 0; j < numConstraints; ++j) {
Vec3 p1 = state.getPositions()[j];
Vec3 p2 = state.getPositions()[j+1];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(1.0, dist, 2e-4);
}
integrator.step(1);
}
}
int main() {
try {
testSingleBond();
testTemperature();
testConstraints();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cuda/tests/TestCudaStandardMMForceField.cpp 0 → 100644
View file @ 5c4a033f
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests all the different force terms in the reference implementation of StandardMMForceField.
*/
#include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h"
#include "CudaPlatform.h"
#include "StandardMMForceField.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testBonds() {
CudaPlatform platform;
System system(3, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(3, 2, 0, 0, 0);
forceField->setBondParameters(0, 0, 1, 1.5, 0.8);
forceField->setBondParameters(1, 1, 2, 1.2, 0.7);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
}
void testAngles() {
CudaPlatform platform;
System system(4, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 2, 0, 0);
forceField->setAngleParameters(0, 0, 1, 2, PI_M/3, 1.1);
forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(2, 1, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double torque1 = 1.1*PI_M/6;
double torque2 = 1.2*PI_M/4;
ASSERT_EQUAL_VEC(Vec3(torque1, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5*torque2, 0.5*torque2, 0), forces[3], TOL); // reduced by sqrt(2) due to the bond length, another sqrt(2) due to the angle
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(0.5*1.1*(PI_M/6)*(PI_M/6) + 0.5*1.2*(PI_M/4)*(PI_M/4), state.getPotentialEnergy(), TOL);
}
void testPeriodicTorsions() {
CudaPlatform platform;
System system(4, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 0, 1, 0);
forceField->setPeriodicTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 2);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double torque = -2*1.1*std::sin(2*PI_M/3);
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, 0), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*PI_M/3)), state.getPotentialEnergy(), TOL);
}
void testRBTorsions() {
CudaPlatform platform;
System system(4, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 0, 0, 1);
forceField->setRBTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double psi = 0.25*PI_M - PI_M;
double torque = 0.0;
for (int i = 1; i < 6; ++i) {
double c = 0.1*(i+1);
torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
}
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
double energy = 0.0;
for (int i = 0; i < 6; ++i) {
double c = 0.1*(i+1);
energy += c*std::pow(std::cos(psi), i);
}
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
void testCoulomb() {
CudaPlatform platform;
System system(2, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(2, 0, 0, 0, 0);
forceField->setAtomParameters(0, 0.5, 1, 0);
forceField->setAtomParameters(1, -1.5, 1, 0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = 138.935485*(-0.75)/4.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(138.935485*(-0.75)/2.0, state.getPotentialEnergy(), TOL);
}
void testLJ() {
CudaPlatform platform;
System system(2, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(2, 0, 0, 0, 0);
forceField->setAtomParameters(0, 0, 1.2, 1);
forceField->setAtomParameters(1, 0, 1.4, 2);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double x = 1.3/2.0;
double eps = SQRT_TWO;
double force = 4.0*eps*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/2.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0)), state.getPotentialEnergy(), TOL);
}
void testExclusionsAnd14() {
CudaPlatform platform;
System system(5, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(5, 4, 0, 0, 0);
forceField->setBondParameters(0, 0, 1, 1, 0);
forceField->setBondParameters(1, 1, 2, 1, 0);
forceField->setBondParameters(2, 2, 3, 1, 0);
forceField->setBondParameters(3, 3, 4, 1, 0);
system.addForce(forceField);
for (int i = 1; i < 5; ++i) {
// Test LJ forces
vector<Vec3> positions(5);
const double r = 1.0;
for (int j = 0; j < 5; ++j) {
forceField->setAtomParameters(j, 0, 1.5, 0);
positions[j] = Vec3(0, j, 0);
}
forceField->setAtomParameters(0, 0, 1.5, 1);
forceField->setAtomParameters(i, 0, 1.5, 1);
positions[i] = Vec3(r, 0, 0);
OpenMMContext context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double x = 1.5/r;
double eps = 1.0;
double force = 4.0*eps*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/r;
double energy = 4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0));
if (i == 3) {
force *= 0.5;
energy *= 0.5;
}
if (i < 3) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
// Test Coulomb forces
forceField->setAtomParameters(0, 2, 1.5, 0);
forceField->setAtomParameters(i, 2, 1.5, 0);
OpenMMContext context2(system, integrator, platform);
context2.setPositions(positions);
state = context2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces2 = state.getForces();
force = 138.935485*4/(r*r);
energy = 138.935485*4/r;
if (i == 3) {
force /= 1.2;
energy /= 1.2;
}
if (i < 3) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces2[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces2[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
}
void testCutoff() {
CudaPlatform platform;
System system(3, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(3, 0, 0, 0, 0);
forceField->setAtomParameters(0, 1.0, 1, 0);
forceField->setAtomParameters(1, 1.0, 1, 0);
forceField->setAtomParameters(2, 1.0, 1, 0);
forceField->setNonbondedMethod(StandardMMForceField::CutoffNonPeriodic);
const double cutoff = 2.9;
forceField->setCutoffDistance(cutoff);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(0, 3, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
const double force1 = 138.935485*(1.0)*(0.25-2.0*krf*2.0);
const double force2 = 138.935485*(1.0)*(1.0-2.0*krf*1.0);
ASSERT_EQUAL_VEC(Vec3(0, -force1, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, force1-force2, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, force2, 0), forces[2], TOL);
const double energy1 = 138.935485*(1.0)*(0.5+krf*4.0-crf);
const double energy2 = 138.935485*(1.0)*(1.0+krf*1.0-crf);
ASSERT_EQUAL_TOL(energy1+energy2, state.getPotentialEnergy(), TOL);
}
void testCutoff14() {
CudaPlatform platform;
System system(5, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(5, 4, 0, 0, 0);
forceField->setBondParameters(0, 0, 1, 1, 0);
forceField->setBondParameters(1, 1, 2, 1, 0);
forceField->setBondParameters(2, 2, 3, 1, 0);
forceField->setBondParameters(3, 3, 4, 1, 0);
forceField->setNonbondedMethod(StandardMMForceField::CutoffNonPeriodic);
const double cutoff = 3.5;
forceField->setCutoffDistance(cutoff);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
positions[2] = Vec3(2, 0, 0);
positions[3] = Vec3(3, 0, 0);
positions[4] = Vec3(4, 0, 0);
for (int i = 1; i < 5; ++i) {
// Test LJ forces
forceField->setAtomParameters(0, 0, 1.5, 1);
for (int j = 1; j < 5; ++j)
forceField->setAtomParameters(j, 0, 1.5, 0);
forceField->setAtomParameters(i, 0, 1.5, 1);
context.reinitialize();
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double r = positions[i][0];
double x = 1.5/r;
double e = 1.0;
double force = 4.0*e*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/r;
double energy = 4.0*e*(std::pow(x, 12.0)-std::pow(x, 6.0));
if (i == 3) {
force *= 0.5;
energy *= 0.5;
}
if (i < 3 || r > cutoff) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
// Test Coulomb forces
const double q = 0.7;
forceField->setAtomParameters(0, q, 1.5, 0);
forceField->setAtomParameters(i, q, 1.5, 0);
context.reinitialize();
context.setPositions(positions);
state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces2 = state.getForces();
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
force = 138.935485*q*q*(1.0/(r*r)-2.0*krf*r);
energy = 138.935485*q*q*(1.0/r+krf*r*r-crf);
if (i == 3) {
force /= 1.2;
energy /= 1.2;
}
if (i < 3 || r > cutoff) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces2[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces2[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
}
void testPeriodic() {
CudaPlatform platform;
System system(3, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(3, 1, 0, 0, 0);
forceField->setAtomParameters(0, 1.0, 1, 0);
forceField->setAtomParameters(1, 1.0, 1, 0);
forceField->setAtomParameters(2, 1.0, 1, 0);
forceField->setBondParameters(0, 0, 1, 1.0, 0.0);
forceField->setNonbondedMethod(StandardMMForceField::CutoffPeriodic);
const double cutoff = 2.0;
forceField->setCutoffDistance(cutoff);
forceField->setPeriodicBoxSize(4.0, 4.0, 4.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
positions[2] = Vec3(3, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
const double force = 138.935485*(1.0)*(1.0-2.0*krf*1.0);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(2*138.935485*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
}
int main() {
try {
testBonds();
testAngles();
testPeriodicTorsions();
testRBTorsions();
testCoulomb();
testLJ();
testExclusionsAnd14();
// testCutoff();
// testCutoff14();
// testPeriodic();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/reference/tests/TestReferenceStandardMMForceField.cpp
View file @ 5c4a033f
......@@ -206,21 +206,19 @@ void testExclusionsAnd14() {
forceField->setBondParameters(3, 3, 4, 1, 0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(5);
const double r = 1.0;
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(r, 0, 0);
positions[2] = Vec3(r, 0, 0);
positions[3] = Vec3(r, 0, 0);
positions[4] = Vec3(r, 0, 0);
for (int i = 1; i < 5; ++i) {
// Test LJ forces
forceField->setAtomParameters(0, 0, 1.5, 1);
for (int j = 1; j < 5; ++j)
vector<Vec3> positions(5);
const double r = 1.0;
for (int j = 0; j < 5; ++j) {
forceField->setAtomParameters(j, 0, 1.5, 0);
positions[j] = Vec3(0, j, 0);
}
forceField->setAtomParameters(0, 0, 1.5, 1);
forceField->setAtomParameters(i, 0, 1.5, 1);
positions[i] = Vec3(r, 0, 0);
context.reinitialize();
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
......
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